MetaLandSim-package |
Landscape And Range Expansion Simulation |
accept.calculate |
Calculate acceptance rates in MCMC chains |
addpoints |
Add a given number of patches to a landscape |
cabrera |
Modified patch occupancy data of Cabrera vole |
calcmode |
Function for mode estimation of a continuous variable |
cluster.graph |
Delivers the number of patches per cluster |
cluster.id |
Classify patches in clusters |
coda.create |
Create files for use with R-package coda. |
combine.chains |
Combines two chains into a single chain. |
components.graph |
Number of components of a landscape |
convert.graph |
Convert data frame to landscape |
create.parameter.df |
Create parameter data frame |
edge.graph |
Produce an edge (links) data frame |
expansion |
Class 'expansion' |
extract.graph |
Extract landscape from span.graph generated list |
ifm.missing.MCMC |
Estimate the 'missing' design incidence function model |
ifm.naive.MCMC |
Estimate the naive design incidence function model |
ifm.robust.MCMC |
Estimate the robust design incidence function model |
import.shape |
Import a shapefile |
iterate.graph |
Simulate landscape series occupation |
landscape |
Class 'landscape' |
landscape_change |
Landscape loosing 5% of patches per time step |
list.stats |
Returning information on a dynamic landscape list |
manage_expansion_sim |
Simulate range expansion simulation |
manage_landscape_sim |
Batch landscape simulation |
matrix.graph |
Returning a matrix with information on connections between patches |
mc_df |
Modified patch occupancy data of Cabrera vole as a data frame |
merge_order |
Internal functions for the MetaLandSim package. |
MetaLandSim |
Landscape And Range Expansion Simulation |
metapopulation |
Class 'metapopulation' |
metrics.graph |
Computes landscape connectivity metrics |
min_distance |
Computes topological distance |
occ.landscape |
Sample landscape with one simulated occupancy snapshot |
occ.landscape2 |
Sample landscape with 10 simulated occupancy snapshots |
param1 |
Sample parameter data frame number 1 |
param2 |
Sample parameter data frame number 2 |
parameter.estimate |
Estimate parameters |
plotL.graph |
Plot one landscape of the list created by span.graph |
plot_expansion |
Graphical display of the expansion simulations |
plot_graph |
Graphical display of the landscape |
range_expansion |
Computes a range expansion model |
range_raster |
Probability of occupancy, dispersal model |
remove.species |
Remove the species occupancy from the landscape |
removepoints |
Remove a given number of patches from the landscape |
rg_exp |
List with range.expansion output |
rland |
Random landscape |
rland.graph |
Creates random landscape graph |
sim.area |
Vector of the areas for each site; here, 100 sites |
sim.det.20 |
Array corresponding to nsites x nyears x nvisits |
sim.distance |
Distance matrix between sampling sites (nsite x nsite). |
simulatedifm |
Set of simulated data to use with the IFM parameter estimation functions. The data were generated using the code provided in "details". |
simulate_graph |
Simulate species occupancy in one dynamic landscape |
span.graph |
Simulate landscape dynamics over a number of time steps |
species.graph |
Simulate landscape occupation |
spom |
Stochastic Patch Occupancy Model |
summary_landscape |
Summarize 'landscape' class objects |
summary_metapopulation |
Summarize 'metapopulation' class objects |
z.sim |
Occupancy data generated with perfect detection. |
z.sim.20 |
Occupancy data generated with perfect detection with approximately 20% of data missing at random. |
z.sim.20.fa |
Occupancy data containing false absences |